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From: Richard Stallman <rms@gnu.org>
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Subject: Re: Building emacs with and without X -- packaging question.
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These differences in cus-load.el are strange.  The code that
updates it is in lisp/Makefile.in, in the custom-deps target;
it works by invoking Lisp code in cus-dep.el.  This code works
by scanning a list of directories.  Can you arrange to see the
list of directories in both cases, and compare them?
If they are different, can you find out where the difference
originates from?